McClean: Making Nice Bar Plots

Summary

This explains the basics of making pretty bar plots in Matlab. The Matlab "bar" command is used, along with some nice scripts discovered on the Matlab file exchange.

Example

Suppose you have some experimental data from two strains (Strain 1 and Strain 2) under four different experiment conditions (Condition A,B,C,D). The means and standard deviations of your measurement of interest look like:

Strain1_Mean=[0.5137    3.2830    1.5887    5.9188];
Strain2_Mean=[0.4042    2.9884    0.5709    2.7766];
Strain1_std=[1.1393    2.8108    2.2203    3.5233];
Strain2_std=[0.8762    2.8478    0.9878    2.2197];

Use Matlab's bar command to plot this data (without error bars) as a bar chart:

bar([1 2 3 4],[Strain1_Mean' Strain2_Mean'])
legend('Strain 1','Strain 2')
pause; close all;

This looks ok, but we would really like some error bars, so we use a handy function from the file exchange:

h=figure; hold;
barwitherr([Strain1_std' Strain2_std'], [1 2 3 4],[Strain1_Mean' Strain2_Mean'])
legend('Strain 1','Strain 2')
pause; close all;

This is ok, but we'd rather only have one-sided error bars. To do this, you will send barwitherr zeros for the lower error and keep the upper error as is by sending in the matrix cat(3,zeros(4,2),[Strain1_std' Strain2_std']) for the error

barwitherr(cat(3,zeros(4,2),[Strain1_std' Strain2_std']), [1 2 3 4],[Strain1_Mean' Strain2_Mean'])
legend('Strain 1','Strain 2')
pause; close all;

Don't like the colors? You can change them by modifying the colormap:

barmap=[0.7 0.7 0.7; 0.05 .45 0.1]; %[0.7 0.7 0.7] is grey, [ 0.05 .45 0.1] is a green
colormap(barmap);
ylabel('Data','FontSize',14)
title('Title of Experiment','FontSize',14)
pause; 

It isn't very useful to have our experimental conditions labelled 1,2,3,4 so can we change these to words? Yes:

set(ax, 'XTick',[1 2 3 4],'XTickLabel',{'A','B','C','D' });
pause;

But this isn't perfect, maybe we want more information on the axis. To have actual labels rotate them using the handy xticklabel_rotate function:

set(ax, 'FontSize',12,'XTick',[1 2 3 4],'XTickLabel',{'Condition A','Condition B','Condition C','Condition D' });
xticklabel_rotate([1 2 3 4],45,{'Condition A','Condition B','Condition C','Condition D' })
pause

If you are going to use this figure in a presentation or paper you can save it in various forms (including as a file for adobe illustrator). Recall that h is our figure handle:

saveas(h, 'ExampleBar.fig','fig')
saveas(h, 'ExampleBar.png','png')
saveas(h, 'ExampleBar.ai','ai')
close all;
 

Code

close all;

%Suppose you have the following data for two different strains across 4
%different experimental conditions (Conditions A,B,C,D, from left to right)
Strain1_Mean=[0.5137    3.2830    1.5887    5.9188];
Strain2_Mean=[0.4042    2.9884    0.5709    2.7766];
Strain1_std=[1.1393    2.8108    2.2203    3.5233];
Strain2_std=[0.8762    2.8478    0.9878    2.2197];


%Plot this data as a bar chart
bar([1 2 3 4],[Strain1_Mean' Strain2_Mean'])
legend('Strain 1','Strain 2')
pause; close all;

%This looks ok, but we would really like some error bars, so we use a handy
%function from the file exchange:
h=figure; hold;
barwitherr([Strain1_std' Strain2_std'], [1 2 3 4],[Strain1_Mean' Strain2_Mean'])
legend('Strain 1','Strain 2')
pause; close all;

%This is ok, but we'd rather only have one-sided error bars.  To do this,
%you will send barwitherr zeros for the lower error and keep the upper
%error as is by sending in the matrix cat(3,zeros(4,2),[Strain1_std'
%Strain2_std']) for the error
barwitherr(cat(3,zeros(4,2),[Strain1_std' Strain2_std']), [1 2 3 4],[Strain1_Mean' Strain2_Mean'])
legend('Strain 1','Strain 2')
pause; close all;

%Now let's use better colors by changing the color map and set the bar
%widths, line widths, axis fonts etc to something prettier
barwitherr(cat(3,zeros(4,2),[Strain1_std' Strain2_std']), [1 2 3 4],[Strain1_Mean' Strain2_Mean'],'LineWidth',2,'BarWidth',0.9)
legend('Strain 1','Strain 2')
%set the axis properties
ax=gca;
set(ax, 'FontSize',12)


%Don't like the colors? You can change them by modifying the colormap:
barmap=[0.7 0.7 0.7; 0.05 .45 0.1]; %[0.7 0.7 0.7] is grey, [ 0.05 .45 0.1] is a green
colormap(barmap);
ylabel('Data','FontSize',14)
title('Title of Experiment','FontSize',14)
pause; 

%It isn't very useful to have our experimental conditions labelled 1,2,3,4
%so can we change these to words? Yes:
set(ax, 'XTick',[1 2 3 4],'XTickLabel',{'A','B','C','D' });
pause;
%But this isn't perfect, maybe we want more information on the axis.  To
%have actual labels rotate them using the handy xticklabel_rotate function:
%set(ax, 'FontSize',12,'XTick',[1 2 3 4],'XTickLabel',{'Condition A','Condition B','Condition C','Condition D' });
xticklabel_rotate([1 2 3 4],45,{'Condition A','Condition B','Condition C','Condition D' })
pause

%If you are going to use this figure in a presentation or paper you can
%save it in various forms (including as a file for adobe illustrator):

%Recall that h is our figure handle:
 saveas(h, 'ExampleBar.fig','fig')
 saveas(h, 'ExampleBar.png','png')
 saveas(h, 'ExampleBar.ai','ai')
 
 close all;
<\pre>

Notes
Please feel free to post comments, questions, or improvements to this protocol. Happy to have your input!

*Megan N McClean 17:27, 30 January 2012 (EDT): Obviously this is nothing fancy, but the code has come in handy for me a number of times, so I thought I would stick it on the wiki in case it is useful to anyone else in the lab.

References
Mathworks Online Help: plotyy

Matlab Newsreader: Plotyy with errorbar

Contact
*Megan N McClean 14:01, 30 January 2012 (EDT)

or instead, discuss this protocol.